Rai wakes up from 820-years long sleep and starts his new life as a student in a high school founded by his loyal servant, Frankenstein. But his peaceful days with other human students are soon interrupted by mysterious attackers known as the “Unions”.

009 Re:Cyborg follows a group of nine cyborgs, each of them created by a shadowy organization for use as weapons against humanity. The group turns on their creators to protect the population instead, using the powers given them to fight their creators.